data_EW3 # _chem_comp.id EW3 _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 F N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-02-10 _chem_comp.pdbx_modified_date 2021-06-04 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 328.188 _chem_comp.one_letter_code ? _chem_comp.three_letter_code EW3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6LWP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal EW3 F2 F1 F 0 1 N N N -3.827 -14.211 32.509 1.845 -3.271 -0.201 F2 EW3 1 EW3 "C2'" C1 C 0 1 N N R -3.871 -15.555 32.432 1.276 -2.114 0.342 "C2'" EW3 2 EW3 "C3'" C2 C 0 1 N N R -5.092 -16.042 31.676 -0.235 -2.319 0.590 "C3'" EW3 3 EW3 "O3'" O1 O 0 1 N N N -6.266 -15.274 32.006 -0.634 -3.634 0.195 "O3'" EW3 4 EW3 "C1'" C3 C 0 1 N N R -4.080 -16.180 33.811 1.336 -0.952 -0.674 "C1'" EW3 5 EW3 "O4'" O2 O 0 1 N N N -4.803 -17.417 33.576 0.095 -0.236 -0.489 "O4'" EW3 6 EW3 "C4'" C4 C 0 1 N N R -5.249 -17.450 32.224 -0.910 -1.257 -0.306 "C4'" EW3 7 EW3 "C5'" C5 C 0 1 N N N -4.388 -18.488 31.528 -2.140 -0.674 0.392 "C5'" EW3 8 EW3 "O5'" O3 O 0 1 N N N -4.650 -18.507 30.131 -2.815 0.218 -0.497 "O5'" EW3 9 EW3 P P1 P 0 1 N N N -4.011 -19.728 29.351 -4.155 1.013 -0.091 P EW3 10 EW3 OP2 O4 O 0 1 N N N -4.403 -21.069 29.928 -4.708 1.819 -1.371 OP2 EW3 11 EW3 OP1 O5 O 0 1 N N N -4.319 -19.459 27.870 -5.181 0.050 0.366 OP1 EW3 12 EW3 N1 N1 N 0 1 N N N -2.867 -16.442 34.624 2.476 -0.080 -0.385 N1 EW3 13 EW3 C2 C6 C 0 1 N N N -2.910 -16.224 35.941 2.504 0.615 0.764 C2 EW3 14 EW3 O2 O6 O 0 1 N N N -3.440 -15.247 36.432 1.633 0.428 1.591 O2 EW3 15 EW3 N3 N2 N 0 1 N N N -2.381 -17.189 36.717 3.471 1.511 1.022 N3 EW3 16 EW3 C4 C7 C 0 1 N N N -1.814 -18.305 36.226 4.310 1.923 0.053 C4 EW3 17 EW3 O4 O7 O 0 1 N N N -1.344 -19.161 36.954 5.226 2.669 0.322 O4 EW3 18 EW3 C5 C8 C 0 1 N N N -1.748 -18.499 34.719 4.109 1.455 -1.366 C5 EW3 19 EW3 C6 C9 C 0 1 N N N -1.731 -17.126 34.019 3.573 0.018 -1.350 C6 EW3 20 EW3 O1 O8 O 0 1 N Y N -2.432 -19.545 29.643 -3.825 2.051 1.095 O1 EW3 21 EW3 H1 H1 H 0 1 N N N -2.963 -15.974 31.974 1.783 -1.839 1.267 H1 EW3 22 EW3 H2 H2 H 0 1 N N N -4.902 -16.062 30.593 -0.478 -2.147 1.638 H2 EW3 23 EW3 H3 H3 H 0 1 N N N -6.174 -14.392 31.666 -0.239 -4.340 0.725 H3 EW3 24 EW3 H4 H4 H 0 1 N N N -4.731 -15.503 34.383 1.404 -1.341 -1.690 H4 EW3 25 EW3 H5 H5 H 0 1 N N N -6.306 -17.751 32.167 -1.188 -1.692 -1.266 H5 EW3 26 EW3 H6 H6 H 0 1 N N N -4.608 -19.480 31.950 -2.814 -1.483 0.676 H6 EW3 27 EW3 H7 H7 H 0 1 N N N -3.328 -18.246 31.693 -1.828 -0.131 1.285 H7 EW3 28 EW3 H8 H8 H 0 1 N N N -4.813 -21.597 29.253 -5.516 2.323 -1.199 H8 EW3 29 EW3 H9 H9 H 0 1 N N N -2.411 -17.070 37.709 3.567 1.866 1.919 H9 EW3 30 EW3 H10 H10 H 0 1 N N N -2.627 -19.069 34.385 3.394 2.107 -1.867 H10 EW3 31 EW3 H11 H11 H 0 1 N N N -0.833 -19.052 34.461 5.061 1.482 -1.897 H11 EW3 32 EW3 H12 H12 H 0 1 N N N -1.866 -17.233 32.933 4.371 -0.668 -1.063 H12 EW3 33 EW3 H13 H13 H 0 1 N N N -0.792 -16.590 34.221 3.208 -0.245 -2.343 H13 EW3 34 EW3 H14 H14 H 0 1 N N N -1.987 -19.304 28.839 -3.159 2.713 0.864 H14 EW3 35 # # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal EW3 OP1 P DOUB N N 1 EW3 P OP2 SING N N 2 EW3 P "O5'" SING N N 3 EW3 "O5'" "C5'" SING N N 4 EW3 "C5'" "C4'" SING N N 5 EW3 "C3'" "O3'" SING N N 6 EW3 "C3'" "C4'" SING N N 7 EW3 "C3'" "C2'" SING N N 8 EW3 "C4'" "O4'" SING N N 9 EW3 "C2'" F2 SING N N 10 EW3 "C2'" "C1'" SING N N 11 EW3 "O4'" "C1'" SING N N 12 EW3 "C1'" N1 SING N N 13 EW3 C6 N1 SING N N 14 EW3 C6 C5 SING N N 15 EW3 N1 C2 SING N N 16 EW3 C5 C4 SING N N 17 EW3 C2 O2 DOUB N N 18 EW3 C2 N3 SING N N 19 EW3 C4 N3 SING N N 20 EW3 C4 O4 DOUB N N 21 EW3 P O1 SING N N 22 EW3 "C2'" H1 SING N N 23 EW3 "C3'" H2 SING N N 24 EW3 "O3'" H3 SING N N 25 EW3 "C1'" H4 SING N N 26 EW3 "C4'" H5 SING N N 27 EW3 "C5'" H6 SING N N 28 EW3 "C5'" H7 SING N N 29 EW3 OP2 H8 SING N N 30 EW3 N3 H9 SING N N 31 EW3 C5 H10 SING N N 32 EW3 C5 H11 SING N N 33 EW3 C6 H12 SING N N 34 EW3 C6 H13 SING N N 35 EW3 O1 H14 SING N N 36 # # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor EW3 InChI InChI 1.03 "InChI=1S/C9H14FN2O8P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)12-2-1-5(13)11-9(12)15/h4,6-8,14H,1-3H2,(H,11,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" EW3 InChIKey InChI 1.03 QEKJBDVYKHPUGN-XVFCMESISA-N EW3 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O" EW3 SMILES CACTVS 3.385 "O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O" EW3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F" EW3 SMILES "OpenEye OEToolkits" 2.0.7 "C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)F" # _pdbx_chem_comp_identifier.comp_id EW3 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)-1,3-diazinan-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site EW3 "Create component" 2020-02-10 PDBJ EW3 "Initial release" 2021-06-09 RCSB ##